from pathlib import Path import pytest from nwb_linkml.adapters import NamespacesAdapter, SchemaAdapter from nwb_schema_language import Attribute, Dataset, FlatDtype, Group, Namespace, Namespaces, Schema @pytest.mark.parametrize( ["class_name", "schema_file", "namespace_name"], [ ("DynamicTable", "table.yaml", "hdmf-common"), ("Container", "base.yaml", "hdmf-common"), ("TimeSeries", "nwb.base.yaml", "core"), ("ImageSeries", "nwb.image.yaml", "core"), ], ) def test_find_type_source(nwb_core_fixture, class_name, schema_file, namespace_name): defining_sch = nwb_core_fixture.find_type_source(class_name) assert defining_sch.path.name == schema_file assert namespace_name == defining_sch.namespace def test_populate_imports(nwb_core_fixture): nwb_core_fixture._populate_imports() schema: SchemaAdapter assert len(nwb_core_fixture.schemas) > 0 for schema in nwb_core_fixture.schemas: need_imports = [ nwb_core_fixture.find_type_source(cls.neurodata_type_def).namespace for cls in schema.created_classes if cls.neurodata_type_inc is not None ] need_imports = [i for i in need_imports if i != schema.namespace] for i in need_imports: assert i in schema.imports def test_build(nwb_core_fixture): pass def test_skip_imports(nwb_core_fixture): """ We can build just the namespace in question without also building the other namespaces that it imports """ res = nwb_core_fixture.build(skip_imports=True) # we shouldn't have any of the hdmf-common schema in with us namespaces = [sch.annotations["namespace"].value for sch in res.schemas] assert all([ns == "core" for ns in namespaces]) def test_roll_down_inheritance(): """ Classes should receive and override the properties of their parents when they have neurodata_type_inc Args: nwb_core_fixture: Returns: """ parent_cls = Group( neurodata_type_def="Parent", doc="parent", attributes=[ Attribute(name="a", dims=["a", "b"], shape=[1, 2], doc="a", value="a"), Attribute(name="b", dims=["c", "d"], shape=[3, 4], doc="b", value="b"), ], datasets=[ Dataset( name="data", dims=["a", "b"], shape=[1, 2], doc="data", attributes=[ Attribute(name="c", dtype=FlatDtype.int32, doc="c"), Attribute(name="d", dtype=FlatDtype.int32, doc="d"), ], ) ], ) parent_sch = Schema(source="parent.yaml") parent_ns = Namespaces( namespaces=[ Namespace( author="hey", contact="sup", name="parent", doc="a parent", version="1", schema=[parent_sch], ) ] ) child_cls = Group( neurodata_type_def="Child", neurodata_type_inc="Parent", doc="child", attributes=[Attribute(name="a", doc="a", value="z")], datasets=[ Dataset( name="data", doc="data again", attributes=[Attribute(name="c", doc="c", value="z"), Attribute(name="e", doc="e")], ), ], groups=[Group(name="untyped_child", neurodata_type_inc="Parent", doc="untyped child")], ) child_sch = Schema(source="child.yaml") child_ns = Namespaces( namespaces=[ Namespace( author="hey", contact="sup", name="child", doc="a child", version="1", schema=[child_sch, Schema(namespace="parent")], ) ] ) parent_schema_adapter = SchemaAdapter(path=Path("parent.yaml"), groups=[parent_cls]) parent_ns_adapter = NamespacesAdapter(namespaces=parent_ns, schemas=[parent_schema_adapter]) child_schema_adapter = SchemaAdapter(path=Path("child.yaml"), groups=[child_cls]) child_ns_adapter = NamespacesAdapter( namespaces=child_ns, schemas=[child_schema_adapter], imported=[parent_ns_adapter] ) child_ns_adapter.complete_namespaces() child = child_ns_adapter.get("Child") # overrides simple attrs assert child.doc == "child" # gets unassigned parent attrs assert "b" in [attr.name for attr in child.attributes] # overrides values while preserving remaining values when set attr_a = [attr for attr in child.attributes if attr.name == "a"][0] assert attr_a.value == "z" assert attr_a.dims == parent_cls.attributes[0].dims assert [attr.value for attr in child.attributes if attr.name == "a"][0] == "z" # preserve unset values in child datasets assert child.datasets[0].dtype == parent_cls.datasets[0].dtype assert child.datasets[0].dims == parent_cls.datasets[0].dims # gets undeclared attrs in child datasets assert "d" in [attr.name for attr in child.datasets[0].attributes] # overrides set values in child datasets while preserving unset c_attr = [attr for attr in child.datasets[0].attributes if attr.name == "c"][0] assert c_attr.value == "z" assert c_attr.dtype == FlatDtype.int32 # preserves new attrs assert "e" in [attr.name for attr in child.datasets[0].attributes] # neurodata_type_def is not included in untyped children assert child.groups[0].neurodata_type_def is None # we don't set any of the attrs from the parent class here because we don't override them, # so we don't need to merge them, and we don't want to clutter our linkml models unnecessarily assert child.groups[0].attributes is None